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Single Nucleotide Polymorphisms as Practical Molecular Tools to Support European Chestnut Agrobiodiversity Management.

ABSTRACT: European chestnut orchards are multifunctional agroforestry systems with a key role in environmental management. Their biodiversity is at risk of erosion and farmers do not have enough tools to protect and valorize traditional ecotypes. In particular, cost effective and reliable molecular markers for cultivar identification are lacking. The aim of this research was to develop a new molecular tool for varietal identification in European chestnuts. A set of cultivars was preliminarily characterized to evaluate the range of genetic diversity using random amplified polymorphic DNA (RAPD) markers. The genetic distances indicated a sufficiently wide variability range among tested genotypes and confirmed they were suitable for our goal. A single nucleotide polymorphism (SNP) mining within 64 expressed sequence tags (EST), covering all the linkage groups, was performed by high-resolution melting (HRM) and validated by target resequencing. Fifty-six SNPs were retrieved by monitoring the variability present on the whole set of considered cultivars in loci uniformly distributed on the genome. A subset of 37 SNPs was finally transformed into kompetitive allele-specific PCR (KASP) markers that were successfully evaluated for varietal discrimination. Three assays (C1083, G0115 and A5096) were identified as necessary and sufficient for distinguishing among the tested cultivars. The developed tools can be effectively exploited by stakeholders for improving the management of the European chestnut genetic resources.

SUBMITTER: Nunziata A

PROVIDER: S-EPMC7370276 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Single Nucleotide Polymorphisms as Practical Molecular Tools to Support European Chestnut Agrobiodiversity Management.

Nunziata Angelina A Ruggieri Valentino V Petriccione Milena M De Masi Luigi L

International journal of molecular sciences 20200707 13

European chestnut orchards are multifunctional agroforestry systems with a key role in environmental management. Their biodiversity is at risk of erosion and farmers do not have enough tools to protect and valorize traditional ecotypes. In particular, cost effective and reliable molecular markers for cultivar identification are lacking. The aim of this research was to develop a new molecular tool for varietal identification in European chestnuts. A set of cultivars was preliminarily characterize ...[more]

PMID: 32646057

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Project description:Single-nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in a number of eukaryotic species. Information on the frequency, nature, and distribution of SNPs in plant genomes is limited. Thus, our objectives were (1) to determine SNP frequency in coding and noncoding soybean (Glycine max L. Merr.) DNA sequence amplified from genomic DNA using PCR primers designed to complete genes, cDNAs, and random genomic sequence; (2) to characterize haplotype variation in these sequences; and (3) to provide initial estimates of linkage disequilibrium (LD) in soybean. Approximately 28.7 kbp of coding sequence, 37.9 kbp of noncoding perigenic DNA, and 9.7 kbp of random noncoding genomic DNA were sequenced in each of 25 diverse soybean genotypes. Over the >76 kbp, mean nucleotide diversity expressed as Watterson's theta was 0.00097. Nucleotide diversity was 0.00053 and 0.00111 in coding and in noncoding perigenic DNA, respectively, lower than estimates in the autogamous model species Arabidopsis thaliana. Haplotype analysis of SNP-containing fragments revealed a deficiency of haplotypes vs. the number that would be anticipated at linkage equilibrium. In 49 fragments with three or more SNPs, five haplotypes were present in one fragment while four or less were present in the remaining 48, thereby supporting the suggestion of relatively limited genetic variation in cultivated soybean. Squared allele-frequency correlations (r(2)) among haplotypes at 54 loci with two or more SNPs indicated low genome-wide LD. The low level of LD and the limited haplotype diversity suggested that the genome of any given soybean accession is a mosaic of three or four haplotypes. To facilitate SNP discovery and the development of a transcript map, subsets of four to six diverse genotypes, whose sequence analysis would permit the discovery of at least 75% of all SNPs present in the 25 genotypes as well as 90% of the common (frequency >0.10) SNPs, were identified.

Project description:BackgroundElectronic health record (EHR)-based clinical decision support tools can improve the use of evidence-based clinical guidelines for preeclampsia management that can reduce maternal mortality and morbidity. No study has investigated the organizational capabilities that enable hospitals to use EHR-based decision support tools to manage preeclampsia.ObjectiveTo examine the association of organizational capabilities and hospital adoption of EHR-based decision support tools for preeclampsia management.MethodsCross-sectional analyses of hospitals providing obstetric care in 2017. In total, 739 hospitals responded to the 2017-2018 National Survey of Healthcare Organizations and Systems (NSHOS) and were linked to the 2017 American Hospital Association (AHA) Annual Survey Database and the Area Health Resources File (AHRF). A total of 425 hospitals providing obstetric care across 49 states were included in the analysis. The main outcome was whether a hospital adopted EHR-based clinical decision support tools for preeclampsia management. Hospital organizational capabilities assessed as predictors include EHR functions, adoption of evidence-based clinical treatments, use of quality improvement methods, and dissemination processes to share best patient care practices. Logistic regression estimated the association of hospital organizational capabilities and hospital adoption of EHR-based decision support tools to manage preeclampsia, controlling for hospital structural and patient sociodemographic characteristics.ResultsTwo-thirds of the hospitals (68%) adopted EHR-based decision support tools for preeclampsia, and slightly more than half (56%) of hospitals had a single EHR system. Multivariable regression results indicate that hospitals with a single EHR system were more likely to adopt EHR-based decision support tools for preeclampsia (17.4 percentage points; 95% CI, 1.9 to 33.0; P < .05) than hospitals with a mixture of EHR and paper-based systems. Compared with hospitals having multiple EHRs, on average, hospitals having a single EHR were also more likely to adopt the tools by 9.3 percentage points, but the difference was not statistically significant (95% CI, -1.3 to 19.9). Hospitals with more processes to aid dissemination of best patient care practices were also more likely to adopt EHR-based decision-support tools for preeclampsia (0.4 percentage points; 95% CI, 0.1 to 0.6, for every 1-unit increase in dissemination processes; P < .01).ConclusionStandardized EHRs and policies to disseminate evidence are foundational hospital capabilities that can help advance the use of EHR-based decision support tools for preeclampsia management in the approximately one-third of US hospitals that still do not use them.

Dataset Information

Single Nucleotide Polymorphisms as Practical Molecular Tools to Support European Chestnut Agrobiodiversity Management.

Publications

Single Nucleotide Polymorphisms as Practical Molecular Tools to Support European Chestnut Agrobiodiversity Management.

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